If you read anything about just war theory, you'll soon find a distinction between criteria for jus ad bellum and jus in bello -- and increasingly you also see a distinction between both of these and jus post bellum. The distinction is often put in terms that are quite stark: they are just different lists. This is very strange, though. We can see this partly in the fact that the jus ad bellum list is always much more comprehensive and coherent than the other two; we can also see it if we look at the history, and recognize that the list for jus ad bellum was originally a list of key elements of justice for all activities of warring, not just for choosing to go to war. But most of all we can see it when we recognize that the lists were not just put together at random out of patchwork pieces, but are derived from consideration of what is involved in deliberate activity.
Practical reason is structured by ends and means from the perspective of the agent; we aim at something and go to it. Thus all deliberate activity, whether it is deciding to go to war, or choosing tactics, or anything else, is about the agent, the means, the ends, or the relations among them. By considering the agent, we get the criterion that activities of war must be carried on by the proper authority. (Since positions of authority in this context are means to the ends of society, proper authority is determined in light of ends much broader than those of the activity itself, namely, those of society itself.) The agent must not just be a proper authority, but must be acting qua proper authority; it is from this that the criterion of public declaration originally comes, since the idea behind it is that going to war must be a legal act and promulgation is required for an exercise of law. By considering the end of the activity itself, we get the criterion that activities of war must be for a just cause, i.e., an end that is itself just and derived from common good.
If we're a proper authority with just cause (of any kind -- it's obviously not just in war that authorities need to be working for just causes), then we work backwards in deliberation from this just end to consider what we should do to achieve that end. There are four basic kinds of consideration in assessing means. The first is possibility, i.e., whether there are means that will attain the end at all, from which derives the criterion of feasibility. The second is necessity, whether these means are the ones that have to be used to attain the end, which is needed in this case because activities of war are extreme measures, and this gives us the somewhat misleadingly named criterion of last resort. The third is suitability, i.e., whether the means are themselves consistent with the end, from which we get the criterion of proportionality. And the fourth is disposition, how we ourselves actually dispose ourselves, our actions, and our instruments in the using of means to achieve ends, which gives us the criterion of right intention, whose name derives from the days when 'intention' still retained something of its technical sense of disposition or orientation to an end.
What is quite clear is that none of these cease to be operative when we move from considering going to war to considering how we fight the war in which we are already participating. The results won't be exactly the same, because we will be considering different circumstances, but the basic structure would have to remain intact all the way through. And indeed, if one looks at the typical things listed as criteria for jus in bello, you can see that it has this structure, albeit defectively. Most of them have to do with maintaining proportionality. The criterion that one should not use means malum in se, for instance, is just part of proportionality -- you must use means suitable for and consistent with a just cause. When it is distinguished from 'proportionality in bello', this is typically because 'proportionality in bello' is being used to cover a very restricted element of proportionality. 'Distinction', that one should make distinctions between the combatant status of different people, is just another element of proportionality. (One of the things proportionality requires ad bellum is that you not be indiscriminate in who you fight.) 'Military necessity' is in reality the same thing as last resort, just obscured by the choice of different names, and 'fair treatment of prisoners of war' is just one thing required for right intention. Proper authority doesn't usually get mentioned, but it is obviously just as important in the middle of a war as it is before, as is feasibility. And the same thing goes with jus post bellum: the circumstances are different but the structure should be exactly the same. The same structure required for just action applies to all activities of war, whether it's starting one, fighting one, or ending one.
The criteria are not even strictly distinctive to war; all cases of extreme measures (like national emergency operations or police crackdowns or even acts of civil disobedience) would necessarily have the same basic structure, with just whatever modification of details is needed for taking into account the differences in the circumstances. But while I have read a lot of work in just war theory, I have yet to see anyone really recognize this rather obvious fact, that the criteria are built on a general account of deliberation-based action, just combined with the fact that we are dealing with a measure that is extreme as a matter of law.